Clinical factors associated with composition of lung microbiota and important taxa predicting clinical prognosis in patients with severe community-acquired pneumonia
1. China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing 100029, China 2. Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100029, China 3. Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China 4. Beijing University of Chinese Medicine, Beijing 100029, China 5. Beijing Luhe Hospital, Beijing 101100, China 6. Tsinghua University–Peking University Joint Center for Life Sciences, Beijing 100084, China
Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R2=0.033; P=0.018), followed by acute kidney injury (AKI; R2=0.032; P=0.011) and plasma MIP-1β level (R2=0.027; P=0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients’ lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.
Days from illness onset to admission, median (IQR)
5 (4)
5.5 (4.25)
5 (4)
0.91
Hours from admission to samplingf, median (IQR)
21 (13)
21 (17)
21 (11.5)
0.79
ICU outcomes
ICU length of stay, day, median (IQR)
9 (9.5)
7.5 (5.5)
12 (10.5)
0.03
Death in ICU, n (%)
11 (16.41)
0 (0)
11 (25.58)
0.23
Day 14 mortality, n (%)
8 (11.94)
0 (0)
8 (18.60)
0.06
Plasma biomarker on admission, pg/mL, mean±SD
IL-4
5.64±12.6
4.89±6.19
6.06±15.1
0.34
IL-6
336.30±725.60
95.99±133.02
470.42±875.35
0.00
IL-8
61.50±144.24
19.63±23.81
84.87±175.56
0.56×10−6
MIP-1β
169.01±498.12
117.53±194.91
197.75±605.59
0.30
VEGF-A
1343.97±761.88
1269.44±752.93
1385.56±772.50
0.44
MMP-9
142.34±156.14
118.01±83.77
155.92±184.23
0.89
Tab.1
Fig.1
Fig.2
Fig.3
MV≥2 daysa
Bacteria
The most abundant ZOTU in sequencing
Yes
Acinetobacter baumannii
ZOTU4_f_ Streptococcaceae (38.43%)c
Yes
Acinetobacter baumannii
ZOTU5_f_ Moraxellaceae (87.82%)
Yes
Acinetobacter baumannii, Klebsiella pneumoniae
ZOTU5_f_ Moraxellaceae (37.71%)
Yes
Pseudomonas aeruginosa
ZOTU1_f_ Pseudomonadaceae (98.5%)
Yes
Pseudomonas aeruginosa
ZOTU1_f_ Pseudomonadaceae (83.84%)
Yes
Staphylococcus aureus
ZOTU18_f_ Streptococcaceae (54.3%)
Yes
Staphylococcus aureus
ZOTU10_f_ Staphylococcaceae (29.84%)
No
Pseudomonas aeruginosa
ZOTU18_f_ Streptococcaceae (13.98%)
No
Pseudomonas aeruginosa
ZOTU1_f_ Pseudomonadaceae (69.33%)
No
Pseudomonas aeruginosa
ZOTU1_f_ Pseudomonadaceae (83.92%)
No
Pseudomonas aeruginosa
ZOTU1_f_ Pseudomonadaceae (36.14%)
No
Staphylococcus aureus
ZOTU13_f_ Corynebacteriaceae (15.91%)
No
Staphylococcus aureus
ZOTU10_f_ Staphylococcaceae (59.17%)
No
Streptococcus pneumoniaeb
ZOTU4_f_ Streptococcaceae (98.02%)
No
Streptococcus pneumoniaeb
ZOTU1_f_ Pseudomonadaceae (27.86%)
No
Acinetobacter baumannii
ZOTU5_f_ Moraxellaceae (50.41%)
No
Klebsiella pneumoniae
ZOTU59_f_ Bacteroidaceae (12.28%)
No
Escherichia coli
ZOTU44_f_ Corynebacteriaceae (13.28%)
Tab.2
Fig.4
Variable
Adjusted HRa
95% CI
P value
Pathogen identifiedb
Bacteria only
Reference
Viral–bacterial co-infection
0.37
0.04–3.20
0.37
Virus
0.90
0.18–4.60
0.90
Others
0.79
0.21–3.02
0.73
Richness (continuous)
1.01
1.00–1.02
0.17
Richness (categorical)c
<150
Reference
199–150
0.65
0.15–2.87
0.57
≥200
3.51
0.84–14.64
0.08
Shannon (continuous)
1.43
1.04–1.98
0.03
Shannon (categorical)c
<2
Reference
4.5–2
2.65
0.73–9.67
0.14
>4.5
5.73
1.41–23.26
0.01
Prevotellaceae, 1%d (continuous)
1.14
1.04–1.25
0.006
Prevotellaceae, % (categorical)c
<0.3
Reference
2.4–0.3
3.54
1.06–11.84
0.04
>2.4
8.58
2.15–34.26
0.002
Actinomycetaceae, 1% (continuous)
1.10
1.02–1.18
0.01
Actinomycetaceae, % (categorical)c
<0.005
Reference
0.5–0.005
2.40
0.74–7.77
0.15
>0.5
10.25
2.77–37.87
0.0005
Moraxellaceae, 1% (continuous)
1.00
0.96–1.04
0.89
Staphylococcaceae, 1% (continuous)
0.98
0.94–1.03
0.40
Streptococcaceae, 1% (continuous)
1.01
0.99–1.04
0.35
Pseudomonadaceae, 1% (continuous)
0.99
0.98–1.01
0.23
Enterobacteriaceae, 1% (continuous)
0.95
0.78–1.15
0.58
Tab.3
1
A Liapikou, E Rosales-Mayor, A Torres. The management of severe community acquired pneumonia in the intensive care unit. Expert Rev Respir Med 2014; 8(3): 293–303 https://doi.org/10.1586/17476348.2014.896202
pmid: 24838089
2
R Espinoza, JRLE Silva, A Bergmann, U de Oliveira Melo, FE Calil, RC Santos, JIF Salluh. Factors associated with mortality in severe community-acquired pneumonia: a multicenter cohort study. J Crit Care 2019; 50: 82–86 https://doi.org/10.1016/j.jcrc.2018.11.024
pmid: 30502687
3
J Phua, NC Dean, Q Guo, WS Kuan, HF Lim, TK Lim. Severe community-acquired pneumonia: timely management measures in the first 24 hours. Crit Care 2016; 20(1): 237 https://doi.org/10.1186/s13054-016-1414-2
pmid: 27567896
4
HY Li, Q Guo, WD Song, YP Zhou, M Li, XK Chen, H Liu, HL Peng, HQ Yu, X Chen, N Liu, ZD Lü, LH Liang, QZ Zhao, M Jiang. Mortality among severe community-acquired pneumonia patients depends on combinations of 2007 IDSA/ATS minor criteria. Int J Infect Dis 2015; 38: 141–145 https://doi.org/10.1016/j.ijid.2015.07.026
pmid: 26255891
5
A Torres, JD Chalmers, CS Dela Cruz, C Dominedò, M Kollef, I Martin-Loeches, M Niederman, RG Wunderink. Challenges in severe community-acquired pneumonia: a point-of-view review. Intensive Care Med 2019; 45(2): 159–171 https://doi.org/10.1007/s00134-019-05519-y
pmid: 30706119
6
ES Charlson, K Bittinger, AR Haas, AS Fitzgerald, I Frank, A Yadav, FD Bushman, RG Collman. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 2011; 184(8): 957–963 https://doi.org/10.1164/rccm.201104-0655OC
pmid: 21680950
7
T Zakharkina, I Martin-Loeches, S Matamoros, P Povoa, A Torres, JB Kastelijn, JJ Hofstra, B de Wever, M de Jong, MJ Schultz, PJ Sterk, A Artigas, LDJ Bos. The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia. Thorax 2017; 72(9): 803–810 https://doi.org/10.1136/thoraxjnl-2016-209158
pmid: 28100714
8
RP Dickson, JR Erb-Downward, GB Huffnagle. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med 2014; 2(3): 238–246 https://doi.org/10.1016/S2213-2600(14)70028-1
pmid: 24621685
MM Pettigrew, JF Gent, Y Kong, M Wade, S Gansebom, AM Bramley, S Jain, SLR Arnold, JA McCullers. Association of sputum microbiota profiles with severity of community-acquired pneumonia in children. BMC Infect Dis 2016; 16(1): 317 https://doi.org/10.1186/s12879-016-1670-4
pmid: 27391033
13
AR Panzer, SV Lynch, C Langelier, JD Christie, K McCauley, M Nelson, CK Cheung, NL Benowitz, MJ Cohen, CS Calfee. Lung microbiota is related to smoking status and to development of acute respiratory distress syndrome in critically ill trauma patients. Am J Respir Crit Care Med 2018; 197(5): 621–631 https://doi.org/10.1164/rccm.201702-0441OC
pmid: 29035085
14
RP Dickson, MJ Schultz, T van der Poll, LR Schouten, NR Falkowski, JE Luth, MW Sjoding, CA Brown, R Chanderraj, GB Huffnagle, LDJ Bos; Biomarker Analysis in Septic ICU Patients (BASIC) Consortium. Lung microbiota predict clinical outcomes in critically ill patients. Am J Respir Crit Care Med 2020; 201(5): 555–563 https://doi.org/10.1164/rccm.201907-1487OC
pmid: 31973575
LA Mandell, RG Wunderink, A Anzueto, JG Bartlett, GD Campbell, NC Dean, SF Dowell, TM File Jr, DM Musher, MS Niederman, A Torres, CG Whitney; Infectious Diseases Society of America; American Thoracic Society. Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin Infect Dis 2007; 44(Suppl 2): S27–S72 https://doi.org/10.1086/511159
pmid: 17278083
17
Interventional Pulmonology Group of the Chinese Thoracic Society, Chinese Medical Association. Guideline for diagnostic flexible bronchoscopy in adults (2019). Chin J Tuberc Respir Dis (Zhonghua Jie He He Hu Xi Za Zhi) 2019; 42(8): 573–590 (in Chinese)
pmid: 31378019
18
B Cao, Y Wang, D Wen, W Liu, J Wang, G Fan, L Ruan, B Song, Y Cai, M Wei, X Li, J Xia, N Chen, J Xiang, T Yu, T Bai, X Xie, L Zhang, C Li, Y Yuan, H Chen, H Li, H Huang, S Tu, F Gong, Y Liu, Y Wei, C Dong, F Zhou, X Gu, J Xu, Z Liu, Y Zhang, H Li, L Shang, K Wang, K Li, X Zhou, X Dong, Z Qu, S Lu, X Hu, S Ruan, S Luo, J Wu, L Peng, F Cheng, L Pan, J Zou, C Jia, J Wang, X Liu, S Wang, X Wu, Q Ge, J He, H Zhan, F Qiu, L Guo, C Huang, T Jaki, FG Hayden, PW Horby, D Zhang, C Wang. A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19. N Engl J Med 2020; 382(19): 1787–1799 https://doi.org/10.1056/NEJMoa2001282
pmid: 32187464
19
Y Wang, G Fan, P Horby, F Hayden, Q Li, Q Wu, X Zou, H Li, Q Zhan, C Wang, B Cao; CAP-China Network. Comparative outcomes of adults hospitalized with seasonal influenza A or B virus infection: application of the 7-category ordinal scale. Open Forum Infect Dis 2019; 6(3): ofz053 https://doi.org/10.1093/ofid/ofz053
pmid: 30895200
20
Y Wang, D Zhang, G Du, R Du, J Zhao, Y Jin, S Fu, L Gao, Z Cheng, Q Lu, Y Hu, G Luo, K Wang, Y Lu, H Li, S Wang, S Ruan, C Yang, C Mei, Y Wang, D Ding, F Wu, X Tang, X Ye, Y Ye, B Liu, J Yang, W Yin, A Wang, G Fan, F Zhou, Z Liu, X Gu, J Xu, L Shang, Y Zhang, L Cao, T Guo, Y Wan, H Qin, Y Jiang, T Jaki, FG Hayden, PW Horby, B Cao, C Wang. Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet 2020; 395(10236): 1569–1578 https://doi.org/10.1016/S0140-6736(20)31022-9
pmid: 32423584
21
F Zhou, Y Wang, Y Liu, X Liu, L Gu, X Zhang, Z Pu, G Yang, B Liu, Q Nie, B Xue, J Feng, Q Guo, J Liu, H Fan, J Chen, Y Zhang, Z Xu, M Pang, Y Chen, X Nie, Z Cai, J Xu, K Peng, X Li, P Xiang, Z Zhang, S Jiang, X Su, J Zhang, Y Li, X Jin, R Jiang, J Dong, Y Song, H Zhou, C Wang, B Cao; CAP-China Network. Disease severity and clinical outcomes of community-acquired pneumonia caused by non-influenza respiratory viruses in adults: a multicentre prospective registry study from the CAP-China Network. Eur Respir J 2019; 54(2): 1802406 https://doi.org/10.1183/13993003.02406-2018
pmid: 31164430
22
ND Ferguson, E Fan, L Camporota, M Antonelli, A Anzueto, R Beale, L Brochard, R Brower, A Esteban, L Gattinoni, A Rhodes, AS Slutsky, JL Vincent, GD Rubenfeld, BT Thompson, VM Ranieri. The Berlin definition of ARDS: an expanded rationale, justification, and supplementary material. Intensive Care Med 2012; 38(10): 1573–1582 https://doi.org/10.1007/s00134-012-2682-1
pmid: 22926653
23
M Singer, CS Deutschman, CW Seymour, M Shankar-Hari, D Annane, M Bauer, R Bellomo, GR Bernard, JD Chiche, CM Coopersmith, RS Hotchkiss, MM Levy, JC Marshall, GS Martin, SM Opal, GD Rubenfeld, T van der Poll, JL Vincent, DC Angus. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3). JAMA 2016; 315(8): 801–810 https://doi.org/10.1001/jama.2016.0287
pmid: 26903338
24
A Khwaja. KDIGO clinical practice guidelines for acute kidney injury. Nephron Clin Pract 2012; 120(4): c179–c184
pmid: 22890468
25
JP Donnelly, SC Chen, CA Kauffman, WJ Steinbach, JW Baddley, PE Verweij, CJ Clancy, JR Wingard, SR Lockhart, AH Groll, TC Sorrell, M Bassetti, H Akan, BD Alexander, D Andes, E Azoulay, R Bialek, RW Bradsher Jr, S Bretagne, T Calandra, AM Caliendo, E Castagnola, M Cruciani, M Cuenca-Estrella, CF Decker, SR Desai, B Fisher, T Harrison, CP Heussel, HE Jensen, CC Kibbler, DP Kontoyiannis, BJ Kullberg, K Lagrou, F Lamoth, T Lehrnbecher, J Loeffler, O Lortholary, J Maertens, O Marchetti, KA Marr, H Masur, JF Meis, CO Morrisey, M Nucci, L Ostrosky-Zeichner, L Pagano, TF Patterson, JR Perfect, Z Racil, E Roilides, M Ruhnke, CS Prokop, S Shoham, MA Slavin, DA Stevens, GR Thompson III, JA Vazquez, C Viscoli, TJ Walsh, A Warris, LJ Wheat, PL White, TE Zaoutis, PG Pappas. Revision and update of the consensus definitions of invasive fungal disease from the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium. Clin Infect Dis 2020; 71(6): 1367–1376 https://doi.org/10.1093/cid/ciz1008
pmid: 31802125
26
BJ Kelly, I Imai, K Bittinger, A Laughlin, BD Fuchs, FD Bushman, RG Collman. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome 2016; 4(1): 7 https://doi.org/10.1186/s40168-016-0151-8
pmid: 26865050
27
AG Venier, C Leroyer, C Slekovec, D Talon, X Bertrand, S Parer, S Alfandari, JM Guerin, B Megarbane, C Lawrence, B Clair, A Lepape, M Perraud, P Cassier, D Trivier, A Boyer, V Dubois, J Asselineau, AM Rogues, R Thiébaut; DYNAPYO study group. Risk factors for Pseudomonas aeruginosa acquisition in intensive care units: a prospective multicentre study. J Hosp Infect 2014; 88(2): 103–108 https://doi.org/10.1016/j.jhin.2014.06.018
pmid: 25155240
28
S Hoang, A Georget, J Asselineau, AG Venier, C Leroyer, AM Rogues, R Thiébaut. Risk factors for colonization and infection by Pseudomonas aeruginosa in patients hospitalized in intensive care units in France. PLoS One 2018; 13(3): e0193300 https://doi.org/10.1371/journal.pone.0193300
pmid: 29522559
29
KER Bachta, JP Allen, BH Cheung, CH Chiu, AR Hauser. Systemic infection facilitates transmission of Pseudomonas aeruginosa in mice. Nat Commun 2020; 11(1): 543 https://doi.org/10.1038/s41467-020-14363-4
pmid: 31992714
30
SK Hilton, E Castro-Nallar, M Pérez-Losada, I Toma, TA McCaffrey, EP Hoffman, MO Siegel, GL Simon, WE Johnson, KA Crandall. Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology. Front Microbiol 2016; 7: 484 https://doi.org/10.3389/fmicb.2016.00484
pmid: 27092134
31
S Emonet, V Lazarevic, C Leemann Refondini, N Gaïa, S Leo, M Girard, V Nocquet Boyer, H Wozniak, L Després, G Renzi, K Mostaguir, E Dupuis Lozeron, J Schrenzel, J Pugin. Identification of respiratory microbiota markers in ventilator-associated pneumonia. Intensive Care Med 2019; 45(8): 1082–1092 https://doi.org/10.1007/s00134-019-05660-8
pmid: 31209523
32
LS Chawla, RL Amdur, C Faselis, P Li, PL Kimmel, CE Palant. Impact of acute kidney injury in patients hospitalized with pneumonia. Crit Care Med 2017; 45(4): 600–606 https://doi.org/10.1097/CCM.0000000000002245
pmid: 28291091
F Polverino, ME Laucho-Contreras, H Petersen, V Bijol, LM Sholl, ME Choi, M Divo, V Pinto-Plata, A Chetta, Y Tesfaigzi, BR Celli, CA Owen. A pilot study linking endothelial injury in lungs and kidneys in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2017; 195(11): 1464–1476 https://doi.org/10.1164/rccm.201609-1765OC
pmid: 28085500
35
M Hepokoski, JA Englert, RM Baron, LE Crotty-Alexander, MM Fuster, JR Beitler, A Malhotra, P Singh. Ventilator-induced lung injury increases expression of endothelial inflammatory mediators in the kidney. Am J Physiol Renal Physiol 2017; 312(4): F654–F660 https://doi.org/10.1152/ajprenal.00523.2016
pmid: 28365585
36
PD Rogers, J Thornton, KS Barker, DO McDaniel, GS Sacks, E Swiatlo, LS McDaniel. Pneumolysin-dependent and-independent gene expression identified by cDNA microarray analysis of THP-1 human mononuclear cells stimulated by Streptococcus pneumoniae. Infect Immun 2003; 71(4): 2087–2094 https://doi.org/10.1128/IAI.71.4.2087-2094.2003
pmid: 12654830
37
BA Turturice, HS McGee, B Oliver, M Baraket, BT Nguyen, C Ascoli, R Ranjan, A Rani, DL Perkins, PW Finn. Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction. PLoS One 2017; 12(10): e0184566 https://doi.org/10.1371/journal.pone.0184566
pmid: 29053714
38
ET Zemanick, BD Wagner, CE Robertson, RC Ahrens, JF Chmiel, JP Clancy, RL Gibson, WT Harris, G Kurland, TA Laguna, SA McColley, K McCoy, G Retsch-Bogart, KT Sobush, PL Zeitlin, MJ Stevens, FJ Accurso, SD Sagel, JK Harris. Airway microbiota across age and disease spectrum in cystic fibrosis. Eur Respir J 2017; 50(5): 1700832 https://doi.org/10.1183/13993003.00832-2017
pmid: 29146601
39
TK Tsang, KH Lee, B Foxman, A Balmaseda, L Gresh, N Sanchez, S Ojeda, R Lopez, Y Yang, G Kuan, A Gordon. Association between the respiratory microbiome and susceptibility to influenza virus infection. Clin Infect Dis 2020; 71(5): 1195–1203 https://doi.org/10.1093/cid/ciz968
pmid: 31562814
40
LN Segal, JC Clemente, JC Tsay, SB Koralov, BC Keller, BG Wu, Y Li, N Shen, E Ghedin, A Morris, P Diaz, L Huang, WR Wikoff, C Ubeda, A Artacho, WN Rom, DH Sterman, RG Collman, MJ Blaser, MD Weiden. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol 2016; 1(5): 16031 https://doi.org/10.1038/nmicrobiol.2016.31
pmid: 27572644
41
A Morris, JM Beck, PD Schloss, TB Campbell, K Crothers, JL Curtis, SC Flores, AP Fontenot, E Ghedin, L Huang, K Jablonski, E Kleerup, SV Lynch, E Sodergren, H Twigg, VB Young, CM Bassis, A Venkataraman, TM Schmidt, GM Weinstock; Lung HIV Microbiome Project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013; 187(10): 1067–1075 https://doi.org/10.1164/rccm.201210-1913OC
pmid: 23491408
42
X Li, Y Sun, Y An, R Wang, H Lin, M Liu, S Li, M Ma, C Xiao. Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China. Environ Pollut 2019; 246: 972–979 https://doi.org/10.1016/j.envpol.2018.12.083
pmid: 31126003
43
JM Larsen, DB Steen-Jensen, JM Laursen, JN Søndergaard, HS Musavian, TM Butt, S Brix. Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota. PLoS One 2012; 7(2): e31976 https://doi.org/10.1371/journal.pone.0031976
pmid: 22363778
44
J Thorsen, MA Rasmussen, J Waage, M Mortensen, A Brejnrod, K Bønnelykke, BL Chawes, S Brix, SJ Sørensen, J Stokholm, H Bisgaard. Infant airway microbiota and topical immune perturbations in the origins of childhood asthma. Nat Commun 2019; 10(1): 5001 https://doi.org/10.1038/s41467-019-12989-7
pmid: 31676759
